Table 3

Topological properties of the empirical molecular ecological networks (MENs) of additional miobial communities and their associated random MENsa
Habitats of communitiesb Empirical networks Random networks
Similarity threshold (st) Network size (n) R2 of power law R2 of scaling law Average path (GD) Average Clustering coefficient (avgCC) Modularity & (the number of modules) Average path (GD) Average clustering coefficient (avgCC) Modularity (M)
Functional MENs
Grassland soils under elevated CO2, MN (i) 0.80 254 0.79 0.25 3.09 0.22 0.44 (18) 3.00 ± 0.03 0.099 ± 0.009 0.31 ± 0.01
Grassland soils under ambient CO2, MN (i) 0.80 184 0.88 0.11 4.21 0.10 0.65 (16) 3.84 ± 0.06 0.028 ± 0.007 0.52 ± 0.01
Lake sediment, Lake DePue, WI (ii) 0.92 151 0.85 0.73 3.47 0.09 0.48 (8) 3.46 ± 0.05 0.046 ± 0.010 0.45 ± 0.01
Groundwater, Well 101–2, Oak Ridge, TN (iii) 0.95 107 0.74 0.44 3.12 0.29 0.52 (11) 3.13 ± 0.07 0.081 ± 0.017 0.40 ± 0.01
Groundwater Well 102–2, Oak Ridge, TN (iii) 0.89 140 0.79 0.21 4.22 0.17 0.67 (12) 3.89 ± 0.08 0.033 ± 0.012 0.53 ± 0.01
Groundwater Well 102–3, Oak Ridge, TN (iii) 0.87 117 0.85 0.19 3.57 0.25 0.64 (13) 3.54 ± 0.09 0.049 ± 0.013 0.48 ± 0.01
Phylogenetic MENs (454 pyrosequencing)
Grassland soils under warming, Norman, OK (iv) 0.76 177 0.83 0.48 3.91 0.13 0.67 (18) 3.94 ± 0.20 0.020 ± 0.008 0.44 ± 0.01
Grassland soils under unwarming, Norman, OK (iv) 0.76 152 0.88 0.10 2.71 0.09 0.61 (20) 3.39 ± 0.23 0.038 ± 0.010 0.47 ± 0.01
Grassland soils under elevated CO2, MN (i) 0.78 263 0.89 0.26 3.95 0.25 0.81 (34) 3.98 ± 0.22 0.015 ± 0.006 0.61 ± 0.02
Grassland soils under ambient CO2, MN (i) 077 292 0.87 0.22 4.26 0.27 0.85 (36) 4.10 ± 0.20 0.017 ± 0.005 0.59 ± 0.01
Agricultural soil, Africa (v) 0.77 384 0.86 0.20 4.99 0.34 0.86 (32) 3.99 ± 0.04 0.020 ± 0.004 0.48 ± 0.01
Human intestine, Stanford, CA (vi) 0.86 215 0.92 0.18 3.55 0.13 0.69 (27) 4.23 ± 0.10 0.025 ± 0.009 0.58 ± 0.01

aVarious parameters of the empirical networks and generation of random networks are explained in the Table 1.

bSample sources: (i) the grassland soils under elevated and ambient CO2 were collected from a free-air CO2 enrichment field in Minnesota which were analyzed with both GeoChip3.0 and 16 S pyrosequencing [49]. The fMENs analysis was desibed in Zhou et al. [27] and pMENs analysis was desibed in Zhou et al. [28]. (ii) The lake sediment samples from Lake DePue were analyzed with GeoChip 2.0. (iii) The groundwater samples from three different Wells in Oak Ridge, Tennessee were analyzed with GeoChip 2.0 [50]. (iv) The grassland samples under warming and unwarming were collected from the long term warming experiment at Oklahoma [51] and analyzed with 16 S pyrosequencing [48]. (v) The pyrosequencing data of agricultural soils from Africa and the groundwater samples from Oak Ridge was provided by Dr. Tiedje and his colleagues at Michigan State University. (vi) The human intestine sample from Stanford was desibed elsewhere [52].

Deng et al.

Deng et al. BMC Bioinformatics 2012 13:113   doi:10.1186/1471-2105-13-113

Open Data